Analysis and Visualization of Microbial Communities

Abstract

In one embodiment, a software tool for performing microbiome analyses including accessing microbiome samples, generating a user interface associated with the software tool, wherein the user interface comprises input fields, and wherein each of the input fields corresponds to one or more of a phenotype or a feature associated with the microbiome samples, receiving user inputs to one or more of the input fields via the user interface of the software tool, generating a visualization comprising analysis results associated with the microbiome samples at the user interface, wherein the analysis results are generated based on the user inputs, and outputting an exportable report and software code comprising the generated visualization.

What is claimed is: 
     
         1 . A software tool for performing microbiome analyses, comprising:
 accessing, by the software tool, a plurality of microbiome samples;   generating, by the software tool, a user interface associated with the software tool, wherein the user interface comprises one or more input fields, and wherein each of the input fields corresponds to one or more of a phenotype or a feature associated with the plurality of microbiome samples;   receiving, via the user interface of the software tool, one or more user inputs to one or more of the input fields;   generating, by the software tool at the user interface, a visualization comprising one or more analysis results associated with the plurality of microbiome samples, wherein the one or more analysis results are generated based on the one or more user inputs; and   outputting, by the software tool, an exportable report and software code comprising the generated visualization.   
     
     
         2 . The software tool of  claim 1 , further comprising:
 generating, by the software tool, one or more quality-control plots based on the accessed microbiome samples;   receiving, via the user interface of the software tool, a data-filtering input based on one or more of minimum sample presence, minimum number of features, or minimum number of reads;   generating, by the software tool, a subset of the accessed microbiome samples based on the data-filtering input; and   updating, by the software tool, the one or more quality-control plots based on the subset of the accessed microbiome samples.   
     
     
         3 . The software tool of  claim 1 , further comprising:
 receiving, via the user interface of the software tool, a data-aggregation input specifying a feature level; and   aggregating, by the software tool, the accessed microbiome samples to the specified feature level.   
     
     
         4 . The software tool of  claim 1 , wherein the microbiome analyses comprise an intra-sample analysis comprising investigating microbial composition within a microbiome sample or a group of microbiome samples. 
     
     
         5 . The software tool of  claim 4 , wherein the one or more analysis results comprise one or more of relative abundance, feature abundance, or alpha diversity. 
     
     
         6 . The software tool of  claim 5 , wherein the one or more analysis results comprise relative abundance, wherein the relative abundance comprises one or more abundant features in a bar plot generated based on one or more user-specified analysis parameters, wherein the one or more user-specified analysis parameters comprise one or more of a phenotype, a faceting manner, or a feature, and wherein the bar plot is modifiable based on one or more of a number of features to show, a switch between showing percentage or reads, or a plot width. 
     
     
         7 . The software tool of  claim 5 , wherein the one or more analysis results comprise feature abundance, wherein the feature abundance comprises an individual abundance of a specific feature as a box plot or a categorical scatterplot generated based on one or more user-specified analysis parameters, wherein the one or more user-specified analysis parameters comprise one or more of a phenotype, a faceting manner, or a feature, wherein the box plot or categorical scatterplot is modifiable based on one or more of a switch between showing points or not showing points, a switch between showing log scale or not showing log scale, a switch between showing percentage or reads, or a plot width. 
     
     
         8 . The software tool of  claim 5 , wherein the one or more analysis results comprise alpha diversity, wherein the alpha diversity comprises a measure of a complexity or a diversity within a particular microbiome sample as a box plot generated based on one or more user-specified analysis parameters, wherein the one or more user-specified analysis parameters comprise one or more of a phenotype, a faceting manner, or a feature, and wherein the box plot is modifiable based on one or more of an index, a coloring manner, or a plot width. 
     
     
         9 . The software tool of  claim 1 , wherein the microbiome analyses comprise an inter-sample analysis, the inter-sample analysis comprising determining differences between microbiome samples or a group of microbiome samples. 
     
     
         10 . The software tool of  claim 9 , wherein the one or more analysis results comprise one or more of beta diversity or feature heatmap. 
     
     
         11 . The software tool of  claim 10 , wherein the one or more analysis results comprise beta diversity, wherein the beta diversity comprises a measure of a complexity of communities between microbiome samples based on one or more user-specified analysis parameters, wherein the one or more user-specified analysis parameters comprise one or more of a distance matrix, an Adonis variable, or an Adonis strata, wherein the beta diversity is illustrated as a scatter plot generated based on principle component analysis, and wherein the scatter plot is modifiable based on one or more of a selection of one or more principal components, a coloring ellipse based on a phenotype, a shape based on a phenotype, a point size, or a plot width. 
     
     
         12 . The software tool of  claim 10 , wherein the one or more analysis results comprise feature heatmap, wherein the feature heatmap comprises a visualization on differences and similarities between microbiome samples, wherein the feature heatmap is generated based on one or more of a number of top features sorted by a user-defined criteria or a user selected feature, and wherein the user-defined criteria comprises one or more of variance, Fano factor, or median absolute deviation. 
     
     
         13 . The software tool of  claim 1 , wherein the microbiome analyses comprise a correlation analysis, the correlation analysis comprising a visualization of relationship between two features or a feature and a phenotype in a scatter plot, wherein the correlation analysis is generated based on an association-evaluation method comprising one or more of Spearman, Person, or Kendall, and wherein the correlation analysis is further generated based on one or more user-specified analysis parameters comprising one or more of a base feature, a correlation feature, or a correlation phenotype. 
     
     
         14 . The software tool of  claim 1 , wherein the microbiome analyses comprise a differential abundance analysis, the differential abundance analysis comprising a test of null hypothesis that a mean or mean ranks between groups of microbiome samples are the same for a specific feature, wherein the differential abundance analysis is generated based on one or more user-specified analysis parameters comprising one or more of a testing method, a comparison phenotype, or a comparison level, and wherein the software tool further generates an interactive table for the differential abundance analysis, the interactive table being operable for a user to open feature plots showing specific levels selected by the user. 
     
     
         15 . The software tool of  claim 1 , wherein the microbiome analyses comprise a longitudinal analysis, the longitudinal analysis comprising a comparison of microbial composition across time points or conditions, wherein the longitudinal analysis is generated based on one or more user-specified analysis parameters comprising one or more of a selected feature, a longitudinal phenotype, a phenotype level order, or a phenotype identifier, wherein the software tool further generates an interactive visualization of a feature plot corresponding to the longitudinal analysis, the interactive visualization being operable for a user to select and color one or more specific phenotype identifiers within the feature plot. 
     
     
         16 . The software tool of  claim 1 , wherein the exportable report is generated based on one or more report setting specified by a user, wherein the one or more report settings comprise one or more of a file name, a report title, author information, or introductory text, wherein the exportable report is in a format specified by the user, and wherein the software code is identified as related to a particular analysis of the microbiome analyses. 
     
     
         17 . One or more computer-readable non-transitory storage media embodying software that is operable when executed to:
 access a plurality of microbiome samples;   generate a user interface, wherein the user interface comprises one or more input fields, and wherein each of the input fields corresponds to one or more of a phenotype or a feature associated with the plurality of microbiome samples;   receive, via the user interface, one or more user inputs to one or more of the input fields;   generate, at the user interface, a visualization comprising one or more analysis results associated with the plurality of microbiome samples, wherein the one or more analysis results are generated based on the one or more user inputs; and   output an exportable report and software code comprising the generated visualization.   
     
     
         18 . A system comprising: one or more processors; and a non-transitory memory coupled to the processors comprising instructions executable by the processors, the processors operable when executing the instructions to:
 access a plurality of microbiome samples;   generate a user interface, wherein the user interface comprises one or more input fields, and wherein each of the input fields corresponds to one or more of a phenotype or a feature associated with the plurality of microbiome samples;   receive, via the user interface, one or more user inputs to one or more of the input fields;   generate, at the user interface, a visualization comprising one or more analysis results associated with the plurality of microbiome samples, wherein the one or more analysis results are generated based on the one or more user inputs; and   output an exportable report and software code comprising the generated visualization.   
     
     
         19 . A method comprising, by one or more computing systems:
 preprocessing a plurality of microbiome samples for microbiome analyses to be performed by a software tool;   inputting the processed microbiome samples to the software tool;   using the software tool to perform quality control on the processed microbiome samples;   using the software tool to perform one or more microbiome analyses based on one or more user inputs; and   generating an exportable report comprising analysis results associated with the one or more microbiome analyses.   
     
     
         20 . A method comprising, by one or more computing systems:
 accessing a plurality of microbiome samples;   receiving one or more user-specified analysis parameters associated with a request for a survival analysis, wherein the one or more user-specified analysis parameters comprise one or more of a selected feature, a selected diversity index, a split of groups, or a phenotype;   generating a visualization comprising a result of the survival analysis associated with the plurality of microbiome samples, wherein the result of the survival analysis is generated based on the one or more user-specified analysis parameters; and   generating an exportable report and software code comprising the generated visualization.